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Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England

Author

Listed:
  • Erik Volz

    (Imperial College London)

  • Swapnil Mishra

    (Imperial College London)

  • Meera Chand

    (Public Health England)

  • Jeffrey C. Barrett

    (Wellcome Sanger Institute)

  • Robert Johnson

    (Imperial College London)

  • Lily Geidelberg

    (Imperial College London)

  • Wes R. Hinsley

    (Imperial College London)

  • Daniel J. Laydon

    (Imperial College London)

  • Gavin Dabrera

    (Public Health England)

  • Áine O’Toole

    (University of Edinburgh)

  • Robert Amato

    (Wellcome Sanger Institute)

  • Manon Ragonnet-Cronin

    (Imperial College London)

  • Ian Harrison

    (Public Health England)

  • Ben Jackson

    (University of Edinburgh)

  • Cristina V. Ariani

    (Wellcome Sanger Institute)

  • Olivia Boyd

    (Imperial College London)

  • Nicholas J. Loman

    (Public Health England
    University of Birmingham)

  • John T. McCrone

    (University of Edinburgh)

  • Sónia Gonçalves

    (Wellcome Sanger Institute)

  • David Jorgensen

    (Imperial College London)

  • Richard Myers

    (Public Health England)

  • Verity Hill

    (University of Edinburgh)

  • David K. Jackson

    (Wellcome Sanger Institute)

  • Katy Gaythorpe

    (Imperial College London)

  • Natalie Groves

    (Public Health England)

  • John Sillitoe

    (Wellcome Sanger Institute)

  • Dominic P. Kwiatkowski

    (Wellcome Sanger Institute)

  • Seth Flaxman

    (Imperial College London)

  • Oliver Ratmann

    (Imperial College London)

  • Samir Bhatt

    (Imperial College London
    University of Copenhagen)

  • Susan Hopkins

    (Public Health England)

  • Axel Gandy

    (Imperial College London)

  • Andrew Rambaut

    (University of Edinburgh)

  • Neil M. Ferguson

    (Imperial College London)

Abstract

The SARS-CoV-2 lineage B.1.1.7, designated variant of concern (VOC) 202012/01 by Public Health England1, was first identified in the UK in late summer to early autumn 20202. Whole-genome SARS-CoV-2 sequence data collected from community-based diagnostic testing for COVID-19 show an extremely rapid expansion of the B.1.1.7 lineage during autumn 2020, suggesting that it has a selective advantage. Here we show that changes in VOC frequency inferred from genetic data correspond closely to changes inferred by S gene target failures (SGTF) in community-based diagnostic PCR testing. Analysis of trends in SGTF and non-SGTF case numbers in local areas across England shows that B.1.1.7 has higher transmissibility than non-VOC lineages, even if it has a different latent period or generation time. The SGTF data indicate a transient shift in the age composition of reported cases, with cases of B.1.1.7 including a larger share of under 20-year-olds than non-VOC cases. We estimated time-varying reproduction numbers for B.1.1.7 and co-circulating lineages using SGTF and genomic data. The best-supported models did not indicate a substantial difference in VOC transmissibility among different age groups, but all analyses agreed that B.1.1.7 has a substantial transmission advantage over other lineages, with a 50% to 100% higher reproduction number.

Suggested Citation

  • Erik Volz & Swapnil Mishra & Meera Chand & Jeffrey C. Barrett & Robert Johnson & Lily Geidelberg & Wes R. Hinsley & Daniel J. Laydon & Gavin Dabrera & Áine O’Toole & Robert Amato & Manon Ragonnet-Cron, 2021. "Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England," Nature, Nature, vol. 593(7858), pages 266-269, May.
    • Handle: RePEc:nat:nature:v:593:y:2021:i:7858:d:10.1038_s41586-021-03470-x
    DOI: 10.1038/s41586-021-03470-x
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    Cited by:

    1. Patrick Munk & Christian Brinch & Frederik Duus Møller & Thomas N. Petersen & Rene S. Hendriksen & Anne Mette Seyfarth & Jette S. Kjeldgaard & Christina Aaby Svendsen & Bram Bunnik & Fanny Berglund & , 2022. "Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    2. Mello, Marco & Moscelli, Giuseppe, 2022. "Voting, contagion and the trade-off between public health and political rights: Quasi-experimental evidence from the Italian 2020 polls," Journal of Economic Behavior & Organization, Elsevier, vol. 200(C), pages 1025-1052.
    3. Santiago Justo Arevalo & Carmen Sofia Uribe Calampa & Cinthy Jimenez Silva & Mauro Quiñones Aguilar & Remco Bouckaert & Joao Renato Rebello Pinho, 2023. "Phylodynamic of SARS-CoV-2 during the second wave of COVID-19 in Peru," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    4. H. H. Webster & T. Nyberg & M. A. Sinnathamby & N. Abdul Aziz & N. Ferguson & G. Seghezzo & P. B. Blomquist & J. Bridgen & M. Chand & N. Groves & R. Myers & R. Hope & E. Ashano & J. Lopez-Bernal & D. , 2022. "Hospitalisation and mortality risk of SARS-COV-2 variant omicron sub-lineage BA.2 compared to BA.1 in England," Nature Communications, Nature, vol. 13(1), pages 1-6, December.
    5. Valentina Marziano & Giorgio Guzzetta & Alessia Mammone & Flavia Riccardo & Piero Poletti & Filippo Trentini & Mattia Manica & Andrea Siddu & Antonino Bella & Paola Stefanelli & Patrizio Pezzotti & Ma, 2021. "The effect of COVID-19 vaccination in Italy and perspectives for living with the virus," Nature Communications, Nature, vol. 12(1), pages 1-8, December.
    6. Joel O. Wertheim & Jade C. Wang & Mindy Leelawong & Darren P. Martin & Jennifer L. Havens & Moinuddin A. Chowdhury & Jonathan E. Pekar & Helly Amin & Anthony Arroyo & Gordon A. Awandare & Hoi Yan Chow, 2022. "Detection of SARS-CoV-2 intra-host recombination during superinfection with Alpha and Epsilon variants in New York City," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    7. Dinesh Aggarwal & Ben Warne & Aminu S. Jahun & William L. Hamilton & Thomas Fieldman & Louis Plessis & Verity Hill & Beth Blane & Emmeline Watkins & Elizabeth Wright & Grant Hall & Catherine Ludden & , 2022. "Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    8. Burridge, James & Gnacik, Michał, 2022. "Public efforts to reduce disease transmission implied from a spatial game," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 589(C).
    9. Andreia L. Pinto & Ranjit K. Rai & Jonathan C. Brown & Paul Griffin & James R. Edgar & Anand Shah & Aran Singanayagam & Claire Hogg & Wendy S. Barclay & Clare E. Futter & Thomas Burgoyne, 2022. "Ultrastructural insight into SARS-CoV-2 entry and budding in human airway epithelium," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    10. Wenjuan Dong & Jing Wang & Lei Tian & Jianying Zhang & Erik W. Settles & Chao Qin & Daniel R. Steinken-Kollath & Ashley N. Itogawa & Kimberly R. Celona & Jinhee Yi & Mitchell Bryant & Heather Mead & S, 2023. "Factor Xa cleaves SARS-CoV-2 spike protein to block viral entry and infection," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    11. Kuan-Ying A. Huang & Xiaorui Chen & Arpita Mohapatra & Hong Thuy Vy Nguyen & Lisa Schimanski & Tiong Kit Tan & Pramila Rijal & Susan K. Vester & Rory A. Hills & Mark Howarth & Jennifer R. Keeffe & Ale, 2023. "Structural basis for a conserved neutralization epitope on the receptor-binding domain of SARS-CoV-2," Nature Communications, Nature, vol. 14(1), pages 1-13, December.

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